Both of those are intentional. I didn't want people to be able to change flies while the fly is out on the water, so the game brings in all your line when you open a fly box. Yes, it means you have to strip out line and re-cast, but I felt that was more true to life than the alternative.

As for jerking fish onto land, that happens in the real world as well. Many times I've hooked a small fish and jerked too hard, flopping the fish right onto the bank. The game considers a fish caught once it's been pulled onto the land, even though it may not be right at your feet.